VMD-L Mailing List

From: Stamatia Zavitsanou (zavitsanoustamatia_at_gmail.com)
Date: Tue Jul 17 2018 - 03:59:29 CDT

Hello,
I am trying to generate a PSF file in order to run a NAMD/FEP simulation.
I use input from CGenFF.
I have created the dual topology file (hybrid.rtf which is created after I
have merged the reference with the mutant ligand into one file) and the
complex.pdb file of the protein and the two ligands.
I want to use autopsf and I load the complex.pdb file, the topology of the
two ligands, hybrid.rtf file and these two files that I have found from
CGenFF, toppar_water_ions_namd.str, top_all36_cgenff.rtf. Is this correct?
It only creates a complex007_autopsf-temp.pdb not a final I think it's
because VMD cannot read my hybrid.rtf file. Has anyone tried to do anything
like that?

If not how do you create the PSF file to run a NAMD/FEP simulation?

Thank you,
Matina